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Calcium in PDB 3sbr: Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form with Substrate

Enzymatic activity of Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form with Substrate

All present enzymatic activity of Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form with Substrate:
1.7.99.6;

Protein crystallography data

The structure of Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form with Substrate, PDB code: 3sbr was solved by A.Pomowski, W.G.Zumft, P.M.H.Kroneck, O.Einsle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 95.00 / 2.24
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 96.577, 106.453, 130.876, 111.45, 107.22, 90.72
R / Rfree (%) 17.3 / 22.7

Other elements in 3sbr:

The structure of Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form with Substrate also contains other interesting chemical elements:

Potassium (K) 8 atoms
Chlorine (Cl) 8 atoms
Copper (Cu) 48 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form with Substrate (pdb code 3sbr). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form with Substrate, PDB code: 3sbr:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 3sbr

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Calcium binding site 1 out of 8 in the Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form with Substrate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form with Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca703

b:37.8
occ:1.00
 O A:MET267 2.3 38.9 1.0
OD1 A:ASN324 2.3 33.5 1.0
O A:TYR256 2.4 31.6 1.0
OD1 A:ASP273 2.5 34.2 1.0
OE2 A:GLU259 2.7 31.3 1.0
OE1 A:GLU259 2.8 30.8 1.0
OD2 A:ASP273 2.9 34.7 1.0
CG A:ASP273 3.0 35.0 1.0
CD A:GLU259 3.1 33.1 1.0
C A:TYR256 3.4 31.8 1.0
CG A:ASN324 3.4 29.9 1.0
C A:MET267 3.4 39.5 1.0
ND2 A:ASN324 4.1 28.3 1.0
N A:ASN257 4.2 32.5 1.0
CA A:ASN257 4.2 33.6 1.0
N A:MET268 4.3 40.5 1.0
N A:SER258 4.3 34.2 1.0
ND2 A:ASN270 4.3 44.7 1.0
CA A:TYR256 4.3 31.0 1.0
CA A:MET268 4.4 41.1 1.0
CA A:MET267 4.4 39.4 1.0
CA A:ASN324 4.5 27.8 1.0
N A:ASN324 4.5 27.5 1.0
CB A:ASP273 4.5 35.6 1.0
CB A:ASN324 4.6 28.1 1.0
CG A:GLU259 4.6 35.5 1.0
OG A:SER258 4.7 33.6 1.0
N A:ARG269 4.8 43.1 1.0
C A:ASN257 4.8 34.2 1.0
O A:ASN270 4.8 42.2 1.0
C A:MET268 4.9 42.1 1.0
CB A:MET267 5.0 38.7 1.0

Calcium binding site 2 out of 8 in 3sbr

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Calcium binding site 2 out of 8 in the Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form with Substrate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form with Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca703

b:23.9
occ:1.00
 O B:MET267 2.3 30.5 1.0
O B:HOH2592 2.4 20.7 1.0
O B:TYR256 2.4 23.1 1.0
OE2 B:GLU259 2.4 25.6 1.0
OD1 B:ASP273 2.5 25.6 1.0
OE1 B:GLU259 2.5 25.7 1.0
OD2 B:ASP273 2.6 24.6 1.0
OD1 B:ASN324 2.6 27.3 1.0
CD B:GLU259 2.8 25.4 1.0
CG B:ASP273 2.9 25.1 1.0
C B:TYR256 3.4 23.1 1.0
C B:MET267 3.5 30.9 1.0
CG B:ASN324 3.5 25.4 1.0
ND2 B:ASN324 4.0 27.0 1.0
N B:ASN257 4.3 23.6 1.0
N B:MET268 4.3 31.6 1.0
CA B:MET268 4.3 32.1 1.0
CA B:ASN257 4.3 24.4 1.0
N B:SER258 4.3 25.4 1.0
CA B:TYR256 4.3 22.6 1.0
CG B:GLU259 4.4 27.6 1.0
CB B:ASP273 4.4 25.7 1.0
CA B:MET267 4.4 30.9 1.0
OG B:SER258 4.5 25.3 1.0
N B:ASN324 4.6 22.8 1.0
CA B:ASN324 4.7 23.1 1.0
O B:ASN270 4.7 31.3 1.0
C B:MET268 4.7 32.2 1.0
CB B:ASN324 4.7 23.6 1.0
N B:ARG269 4.8 32.4 1.0
C B:ASN257 4.9 24.9 1.0
CB B:ASN270 4.9 30.7 1.0
N B:ASN270 4.9 31.5 1.0

Calcium binding site 3 out of 8 in 3sbr

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Calcium binding site 3 out of 8 in the Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form with Substrate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form with Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca703

b:11.3
occ:1.00
 O C:TYR256 2.3 10.0 1.0
O C:HOH2673 2.4 8.7 1.0
OD1 C:ASN324 2.4 11.1 1.0
OE2 C:GLU259 2.4 13.2 1.0
OD1 C:ASP273 2.4 15.7 1.0
O C:MET267 2.4 13.7 1.0
OE1 C:GLU259 2.7 10.6 1.0
OD2 C:ASP273 2.7 11.6 1.0
CD C:GLU259 2.9 12.7 1.0
CG C:ASP273 2.9 14.4 1.0
CG C:ASN324 3.3 11.0 1.0
C C:TYR256 3.5 10.0 1.0
C C:MET267 3.6 14.2 1.0
ND2 C:ASN324 3.8 9.4 1.0
N C:ASN257 4.3 9.8 1.0
CA C:TYR256 4.4 10.6 1.0
CA C:ASN257 4.4 10.4 1.0
OG C:SER258 4.4 13.2 1.0
CA C:MET268 4.4 15.9 1.0
N C:MET268 4.4 15.1 1.0
N C:SER258 4.4 11.4 1.0
CB C:ASP273 4.4 13.4 1.0
CG C:GLU259 4.4 13.3 1.0
N C:ASN324 4.5 10.4 1.0
CB C:ASN324 4.5 10.1 1.0
CA C:MET267 4.5 13.9 1.0
CA C:ASN324 4.5 10.4 1.0
O C:ASN270 4.7 16.5 1.0
C C:MET268 4.8 16.0 1.0
N C:ARG269 4.8 16.9 1.0
C C:ASN257 4.9 10.6 1.0
N C:ASN270 4.9 17.2 1.0
CB C:ASN270 5.0 16.9 1.0
CB C:TYR256 5.0 10.3 1.0

Calcium binding site 4 out of 8 in 3sbr

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Calcium binding site 4 out of 8 in the Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form with Substrate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form with Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca703

b:19.7
occ:1.00
 O D:MET267 2.2 27.5 1.0
OD1 D:ASN324 2.4 22.2 1.0
O D:HOH2725 2.4 16.5 1.0
OD1 D:ASP273 2.5 21.9 1.0
O D:TYR256 2.5 20.5 1.0
OE2 D:GLU259 2.6 22.9 1.0
OE1 D:GLU259 2.6 21.5 1.0
OD2 D:ASP273 2.7 21.3 1.0
CG D:ASP273 2.9 22.3 1.0
CD D:GLU259 3.0 23.6 1.0
CG D:ASN324 3.2 21.3 1.0
C D:MET267 3.4 27.8 1.0
C D:TYR256 3.5 20.1 1.0
ND2 D:ASN324 3.7 19.3 1.0
CA D:MET268 4.2 29.5 1.0
N D:MET268 4.2 28.5 1.0
N D:ASN257 4.3 20.8 1.0
CA D:TYR256 4.4 19.7 1.0
CA D:MET267 4.4 27.6 1.0
CA D:ASN257 4.4 21.6 1.0
OG D:SER258 4.4 25.0 1.0
CB D:ASN324 4.5 20.8 1.0
CB D:ASP273 4.5 21.7 1.0
N D:ASN324 4.5 21.4 1.0
O D:ASN270 4.5 30.6 1.0
CA D:ASN324 4.5 20.9 1.0
N D:SER258 4.5 23.2 1.0
CG D:GLU259 4.5 25.3 1.0
C D:MET268 4.7 29.9 1.0
N D:ARG269 4.8 30.5 1.0
N D:ASN270 4.8 30.7 1.0
C D:ASN257 5.0 22.4 1.0
CB D:ASN270 5.0 30.3 1.0

Calcium binding site 5 out of 8 in 3sbr

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Calcium binding site 5 out of 8 in the Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form with Substrate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form with Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca703

b:10.5
occ:1.00
 O E:MET267 2.3 11.7 1.0
O E:TYR256 2.4 11.1 1.0
OD1 E:ASN324 2.4 8.5 1.0
OE2 E:GLU259 2.5 8.4 1.0
OD1 E:ASP273 2.6 11.3 1.0
OD2 E:ASP273 2.6 11.0 1.0
OE1 E:GLU259 2.6 9.8 1.0
CD E:GLU259 2.9 9.8 1.0
CG E:ASP273 3.0 10.9 1.0
C E:MET267 3.4 12.3 1.0
C E:TYR256 3.4 11.1 1.0
CG E:ASN324 3.4 8.1 1.0
ND2 E:ASN324 4.0 8.1 1.0
N E:MET268 4.1 13.2 1.0
CA E:MET268 4.1 13.2 1.0
N E:ASN257 4.3 11.4 1.0
CA E:TYR256 4.3 10.9 1.0
CA E:ASN257 4.3 11.3 1.0
OG E:SER258 4.4 10.2 1.0
CA E:MET267 4.4 12.2 1.0
N E:ASN324 4.5 8.0 1.0
CG E:GLU259 4.5 10.8 1.0
CB E:ASP273 4.5 10.8 1.0
N E:SER258 4.5 11.6 1.0
CA E:ASN324 4.6 8.0 1.0
O E:ASN270 4.6 12.4 1.0
CB E:ASN324 4.6 8.0 1.0
C E:MET268 4.7 12.6 1.0
N E:ASN270 4.8 11.6 1.0
N E:ARG269 4.8 12.8 1.0
C E:ASN257 4.9 11.4 1.0
CB E:ASN270 5.0 11.2 1.0
CB E:TYR256 5.0 10.9 1.0

Calcium binding site 6 out of 8 in 3sbr

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Calcium binding site 6 out of 8 in the Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form with Substrate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form with Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca703

b:13.8
occ:1.00
 OD1 F:ASP273 2.3 13.4 1.0
O F:MET267 2.4 17.6 1.0
O F:HOH2077 2.4 14.2 1.0
OE2 F:GLU259 2.5 16.3 1.0
O F:TYR256 2.5 11.6 1.0
OD1 F:ASN324 2.5 14.3 1.0
OE1 F:GLU259 2.6 15.2 1.0
OD2 F:ASP273 2.6 13.9 1.0
CG F:ASP273 2.8 13.4 1.0
CD F:GLU259 2.9 15.7 1.0
CG F:ASN324 3.5 11.5 1.0
C F:TYR256 3.5 11.8 1.0
C F:MET267 3.5 17.6 1.0
ND2 F:ASN324 4.0 8.2 1.0
N F:ASN257 4.3 12.2 1.0
CB F:ASP273 4.3 13.5 1.0
N F:SER258 4.3 14.5 1.0
OG F:SER258 4.4 15.3 1.0
CA F:MET268 4.4 18.1 1.0
CA F:TYR256 4.4 11.3 1.0
N F:MET268 4.4 17.6 1.0
CA F:ASN257 4.4 13.4 1.0
CG F:GLU259 4.4 16.5 1.0
CA F:MET267 4.5 17.8 1.0
N F:ASN324 4.5 9.5 1.0
O F:ASN270 4.6 16.9 1.0
CA F:ASN324 4.6 9.9 1.0
CB F:ASN324 4.6 10.0 1.0
N F:ARG269 4.8 18.8 1.0
C F:MET268 4.8 18.3 1.0
C F:ASN257 4.8 13.8 1.0
N F:ASN270 5.0 18.1 1.0

Calcium binding site 7 out of 8 in 3sbr

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Calcium binding site 7 out of 8 in the Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form with Substrate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form with Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca703

b:31.5
occ:1.00
 O G:MET267 2.3 34.2 1.0
OD1 G:ASN324 2.4 25.6 1.0
OD1 G:ASP273 2.5 27.6 1.0
OE2 G:GLU259 2.5 27.6 1.0
OE1 G:GLU259 2.5 26.9 1.0
O G:TYR256 2.5 25.7 1.0
OD2 G:ASP273 2.8 27.6 1.0
CD G:GLU259 2.9 28.3 1.0
CG G:ASP273 3.0 27.4 1.0
C G:MET267 3.5 34.9 1.0
CG G:ASN324 3.5 25.4 1.0
C G:TYR256 3.6 25.5 1.0
ND2 G:ASN324 4.0 25.1 1.0
CA G:MET268 4.2 35.5 1.0
N G:MET268 4.3 35.2 1.0
CG G:GLU259 4.4 30.5 1.0
N G:ASN257 4.4 26.2 1.0
CA G:ASN257 4.4 27.2 1.0
CA G:MET267 4.5 34.9 1.0
N G:SER258 4.5 28.5 1.0
CB G:ASP273 4.5 27.9 1.0
CA G:TYR256 4.5 24.9 1.0
O G:ASN270 4.6 36.1 1.0
OG G:SER258 4.6 29.9 1.0
N G:ASN324 4.6 24.8 1.0
CA G:ASN324 4.6 24.1 1.0
CB G:ASN324 4.6 24.2 1.0
C G:MET268 4.7 35.7 1.0
N G:ARG269 4.8 36.6 1.0
N G:ASN270 4.9 36.5 1.0
C G:ASN257 5.0 28.0 1.0

Calcium binding site 8 out of 8 in 3sbr

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Calcium binding site 8 out of 8 in the Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form with Substrate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form with Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca703

b:9.4
occ:1.00
 OE2 H:GLU259 2.3 8.1 1.0
OD1 H:ASP273 2.4 8.4 1.0
O H:TYR256 2.5 7.7 1.0
O H:MET267 2.5 8.3 1.0
OD1 H:ASN324 2.5 10.6 1.0
OD2 H:ASP273 2.6 7.9 1.0
OE1 H:GLU259 2.6 9.0 1.0
CD H:GLU259 2.8 9.1 1.0
CG H:ASP273 2.9 7.9 1.0
C H:TYR256 3.5 7.7 1.0
C H:MET267 3.5 9.2 1.0
CG H:ASN324 3.5 9.2 1.0
ND2 H:ASN324 4.1 7.7 1.0
CA H:MET268 4.2 9.6 1.0
N H:ASN257 4.3 8.0 1.0
N H:MET268 4.3 9.4 1.0
CA H:ASN257 4.3 8.0 1.0
CA H:TYR256 4.3 7.9 1.0
CG H:GLU259 4.3 8.9 1.0
CB H:ASP273 4.4 8.9 1.0
N H:SER258 4.4 8.1 1.0
N H:ASN324 4.5 8.3 1.0
CA H:MET267 4.5 8.8 1.0
OG H:SER258 4.6 10.0 1.0
CA H:ASN324 4.6 8.6 1.0
CB H:ASN324 4.7 8.7 1.0
C H:MET268 4.7 9.5 1.0
O H:ASN270 4.7 10.8 1.0
N H:ARG269 4.8 9.6 1.0
N H:ASN270 4.8 10.3 1.0
CB H:ASN270 4.8 10.0 1.0
C H:ASN257 4.9 7.9 1.0
CB H:TYR256 5.0 7.9 1.0

Reference:

A.Pomowski, W.G.Zumft, P.M.Kroneck, O.Einsle. N2O Binding at A [4CU:2S] Copper-Sulphur Cluster in Nitrous Oxide Reductase. Nature V. 477 234 2011.
ISSN: ISSN 0028-0836
PubMed: 21841804
DOI: 10.1038/NATURE10332
Page generated: Sat Jul 13 19:09:44 2024

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